obtain_mod_MSFragger {PepMapViz} | R Documentation |
Obtain modification information from Peptide data generated by MSFragger
Description
This function takes MSFragger output containing a 'Assigned Modifications' column with PTM information and converts it into a new dataframe with the desired format of peptide sequences and associated PTM information.
Usage
obtain_mod_MSFragger(
data,
mod_column,
seq_column,
PTM_table = NULL,
PTM_annotation = FALSE,
PTM_mass_column
)
Arguments
data |
A data.table with a column containing stripped sequence and a column containing PTM information. |
mod_column |
The name of the column containing the modified peptide sequences. |
seq_column |
The name of the column containing peptide sequences for MSFragger. |
PTM_table |
A data.table with columns 'PTM_mass' and 'PTM_type' containing PTM annotation information. |
PTM_annotation |
A logical value indicating whether to include PTM annotation information in the result. |
PTM_mass_column |
The name of the column containing the PTM mass information |
Value
A data.table with 'PTM_position', 'PTM_type', 'reps', and other columns.
Examples
library(data.table)
data <- data.table(
Peptide = c("DDREDMLVYQAK", "EAAENSLVAYK", "IEAELQDICNDVLELLDK"),
`Assigned Modifications` = c("C-term(15.9949), 6M(-0.98)", "", "N-term(42.0106)"),
Condition1 = c("A", "B", "B"),
Condition2 = c("C", "C", "D")
)
PTM_table <- data.table(
PTM_mass = c(42.0106, -0.98, 15.9949),
PTM_type = c("Acet", "Amid", "Ox")
)
mod_column <- "Assigned Modifications"
seq_column <- "Peptide"
converted_data <- obtain_mod_MSFragger(
data,
mod_column,
seq_column,
PTM_table,
PTM_annotation = TRUE,
PTM_mass_column = "PTM_mass"
)